what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location?

On 8/15/16 4:13 PM, A Nunes wrote:

Hi,

I have read in the mailing list about zero cortical thickness, but I still have some doubts.

I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all subjects is zero, I would guess is not considered cortical, however, all my areas are cortical.

• If I compute a ttest against two groups, should I set the zeros as

NaNs? or are the zero thickness meaningful (a genuine measure or a segmentation artifact)?

-Should I use the -l ?h.cortex.label to avoid having zero thickness in some areas? If so, at which point? the commands used are:

mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h --sval-annot fsaverage/label/?h.areas.annot --tval $SUBJECTS_DIR/subjid/label/?h.areas.annot

mris_anatomical_stats -a $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h

Thanks Adonay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer